- edited description
CreateGermlines.py fails with error 'Germline sequence differs in length from input sequence by X characters.'
Hello,
I was having some problems running buildPhylipLineage as the germline and input sequences were occasionally different lengths. I saw that running CreateGermlines.py may help but I am getting a similar error back, that the germline sequence is a different length to the input sequence.
This is the code I am running:
CreateGermlines.py --format airr -d copybcr_and_seurat1_clone-pass.tsv -g dmask --cloned -r /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHV.fasta /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHD.fasta /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHJ.fasta --log log.txt
The input into this is what I got from DefineClones.py which seemed to work.
Am I missing a step?
Thanks!
Comments (4)
-
reporter -
- changed status to resolved
Hi Elinor. Sorry for the delay. Somehow I missed this issue. The CreateGermlines.py command seems correct. Maybe the issue was with the buildPhylipLineage settings. Notice it takes one clone as input, not the full db. I am closing this issue because it is old (sorry!) and I suspect you have figured a solution yourself. Please, reopen if needed.
-
I have also run into this problem. It works on the same data when
--cloned
is removed.
Edit: I am using CreateGermline.py with scoper output reduced to only the relevant clonal family
-
Are there NAs in the clone_id column? Kelly, can you please send us to immcantation@googlegroups.com example data to reproduce and debug the error?
- Log in to comment